The "brothers war" of 1861 to 1865, when 31 million people of the United States turned upon each other in terrible strife, affected Mennonites and Amish in varied and complex ways. Unprepared for intense war hysteria and military conscription, many found little room remaining for neutrality. No war had arrested their attention for three generations.

Many had become comfortably established in America. Caught up in the spirit of building America or moving west with the frontier, their quiescent piety had little room for Christian education or even church periodicals. Calls for enlistees to "save the Union " found numerous unbaptized young men joining local regiments and marching off to war. Most Mennonites and Amish, however, tried to avoid military service, as nonresistance remained the official position of their churches. Large and strong churches and communities sometimes found that easier to maintain than weaker frontier communities.

From their own records, we learn only a little about how Mennonites and Amish were jolted by feverish and rabid patriotism. Local newspapers and government records here and there reveal more. By the 1860s, many Mennonites had become used to the idea of voting, serving as school directors, and even holding local offices. Generally, Republican Party candidates got the Amish and Mennonite vote. Two notable exceptions were the Hessian Amish at Danvers, Illinois, and the Amish of Holmes County, Ohio, where German Township had a nearly unanimous Democrat Party voting pattern.

Mennonite and Amish historic teachings on nonresistance, paying of taxes, and being loyal to government sometimes became verbal flash points in local communities. After a year of war, by the summer and fall of 1862, there was alarm when the first draft threatened. Many Pennsylvania Mennonites scrambled to file conscientious objector depositions permitted by that state, or they sought physical exemptions. Franconia area ministers went to visit the Pennsylvania governor. In OhioJohn M. Brenneman drafted a petition to President Lincoln and tried to get a fellow minister to take it to Washington. No evidence has been found that it reached Lincoln. Mennonites favored the Union, abhorred rebellion, and were glad to pay a fine, said Brenneman. In Wayne County, Ohio the Sonnenberg congregation held a special meeting to discuss "the present sad state of the country," then sent resolutions to Ohio's governor, offering money and suggesting a commutation fee in lieu of military service. Within several months, a large majority of family heads had given a total of over $1,500 to the local military committee. Fellow Swiss Mennonites at Bluffton petitioned Ohio's governor to levy a reasonable military tax. The Amish of Holmes County, as described by several letters, were said to be wholly nonresistant and would not fight, but they would be happy to pay liberally for substitutes.

Pro-union sentiments tend to be obvious. Amish mothers in the Peoria, Illinois, area even sang a derisive ditty to their children about Jefferson Davis. Samuel Hage's letter from Washington, Iowa, expressed chagrin at southern sympathizers. Minister Peter Nissley of Marietta in Lancaster County, Pennsylvania, had this same opinion. He heard the cannon and watched the burning of the long and magnificent 40-foot wide Columbia bridge across the Susquehanna—a fire set by "our few men" to stop the "Rebels." Throughout the war, Mennonites in Lancaster County were assaulted verbally in the newspapers. Many were successful farmers, and some neighbors failed to understand how Mennonites could vote for Thaddeus Stevens, Republican leader of the House of Representatives—a fire-breathing warmonger—then insist on avoiding military duty by buying substitutes or paying the $300 commutation fee.

John F. Funk, a baptized Mennonite and a Chicago businessman, joined the Wide Awakes Republican Club and at one point considered joining the military, if drafted. After a crucial visit to Indiana Mennonites, he turned from political interests to begin the Herald of Truth, to write Warfare: Its Evils, Our Duty in 1864, and to publish John M. Brenneman's booklet, Christianity and Warfare. Toward the end of the war a few voices began to question whether nonresistant Mennonites should be buying substitutes and paying money so freely.

Virginia Mennonites have a considerably different story, as outlined in Samuel Horst's Mennonites in the Confederacy (Scottdale, 1967). Most were pro-Union, but under duress of life and limb some voted in favor of Virginia seceding from the Union. A few risked voting against it. Some were forced into the military but then refused to shoot at people. Arrests, prison, high fines, and other pressures finally drove quite a few to take flight to the North. Mennonite farmers saw their horses pressed into service, and raiding soldiers took food and supplies. The final and worst outrage came when General Sheridan's raid through the Shenandoah Valley torched more than 2,000 barns, more than 70 mills, and a few houses and devastated food supplies. Numerous families secured passes and transportation northward.